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How to merge sequences with new sequence insertion

1 message · arun

arun
# 
Hi,
Try:

Lines1 <- readLines(textConnection(">contig number 11
tttgctcggaggggatc
gaaaacacttccttattatacaggtaaaccgtatttggat
aaagctcggaggggatcccct")) 


seq1 <- "nnnnncattccattcattaattaattaatgaatgaatgnnnnn"
concatenated_contig <- paste(Lines1[!grepl(">",Lines1)],collapse=seq1)
concatenated_contig
#[1] #"tttgctcggaggggatcnnnnncattccattcattaattaattaatgaatgaatgnnnnngaaaacacttccttattatacaggtaaaccgtatttggatnnnnncattccattcattaattaattaatgaatgaatgnnnnnaaagctcggaggggatcccct"
A.K.



Hi all, 

I have a sequence files with huge number of contigs such as (contig number does not reflect the order):
tttgctcggaggggatc
gaaaacacttccttattatacaggtaaaccgtatttggat
aaagctcggaggggatcccct 
... 
.. 

I want to concatenate the contigs such that the above order is 
preserved, and also, I want to insert the sequence 
"nnnnncattccattcattaattaattaatgaatgaatgnnnnn" in each contig boundaries 
(here are two contig boundaries), such that the final output file would 
become as follows:
tttgctcggaggggatcnnnnncattccattcattaattaattaatgaatgaatgnnnnngaaaacacttccttattatacaggtaaaccgtatttggatnnnnncattccattcattaattaattaatgaatgaatgnnnnnaaagctcggaggggatcccct 

Any help in solving the problem is highly appreciated. Thanks in advance..